Merge #371

371: Update deps r=valeriabarra a=valeriabarra

## Purpose 
Closes #370 

Updates dependencies. In particualar:

```
↑ ClimaAtmos v0.15.4 ⇒ v0.15.5
```

## Content
- Solution implemented:
    - [x] Updated Manifest files
    - [x] Updated ClimaAtmos CLI options    

Review checklist

I have:
- followed the codebase contribution guide: https://clima.github.io/ClimateMachine.jl/latest/Contributing/
- followed the style guide: https://clima.github.io/ClimateMachine.jl/latest/DevDocs/CodeStyle/
- followed the documentation policy: https://github.com/CliMA/policies/wiki/Documentation-Policy
- checked that this PR does not duplicate an open PR.

In the Content, I have included 
- relevant unit tests, and integration tests, 
- appropriate docstrings on all functions, structs, and modules, and included relevant documentation.


----
- [x] I have read and checked the items on the review checklist.


Co-authored-by: Valeria Barra <[email protected]>

experiments/AMIP/modular/Manifest.toml

@@ -10,16 +10,16 @@ uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
 version = "0.1.6"
 
 [[deps.AMD]]
-deps = ["Libdl", "LinearAlgebra", "SparseArrays", "Test"]
-git-tree-sha1 = "00163dc02b882ca5ec032400b919e5f5011dbd31"
+deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse_jll"]
+git-tree-sha1 = "7e075388abb011075d994e735474ebeed0f24c4f"
 uuid = "14f7f29c-3bd6-536c-9a0b-7339e30b5a3e"
-version = "0.5.0"
+version = "0.5.1"
 
 [[deps.AbstractFFTs]]
-deps = ["ChainRulesCore", "LinearAlgebra"]
-git-tree-sha1 = "cad4c758c0038eea30394b1b671526921ca85b21"
+deps = ["ChainRulesCore", "LinearAlgebra", "Test"]
+git-tree-sha1 = "d92ad398961a3ed262d8bf04a1a2b8340f915fef"
 uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c"
-version = "1.4.0"
+version = "1.5.0"
 
 [[deps.AbstractTrees]]
 git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c"
@@ -62,9 +62,9 @@ version = "0.1.29"
 
 [[deps.ArrayLayouts]]
 deps = ["FillArrays", "LinearAlgebra", "SparseArrays"]
-git-tree-sha1 = "0adeb373cb2268a0f4e62d349ce9957b509d4d7e"
+git-tree-sha1 = "6189f7819e6345bcc097331c7db571f2f211364f"
 uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a"
-version = "1.1.0"
+version = "1.1.1"
 
 [[deps.ArtifactWrappers]]
 deps = ["Downloads", "Pkg"]
@@ -77,9 +77,9 @@ uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
 
 [[deps.AtmosphericProfilesLibrary]]
 deps = ["Dierckx"]
-git-tree-sha1 = "0d2fe99b3bc12cb4339e20b01755b24036789845"
+git-tree-sha1 = "66f7e7f704c848d5b09bd11c980bc28d83f75c77"
 uuid = "86bc3604-9858-485a-bdbe-831ec50de11d"
-version = "0.1.2"
+version = "0.1.3"
 
 [[deps.Atomix]]
 deps = ["UnsafeAtomics"]
@@ -101,9 +101,9 @@ version = "0.4.2"
 
 [[deps.BandedMatrices]]
 deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "PrecompileTools", "SparseArrays"]
-git-tree-sha1 = "faf8639a185bed4babd2e688ace992b14ea44a04"
+git-tree-sha1 = "3cddbe0fad23df52587e675b3d71eea66b850cb9"
 uuid = "aae01518-5342-5314-be14-df237901396f"
-version = "0.17.33"
+version = "0.17.34"
 
 [[deps.Base64]]
 uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
@@ -210,9 +210,9 @@ version = "0.1.8"
 
 [[deps.ClimaAtmos]]
 deps = ["ArgParse", "ArtifactWrappers", "Artifacts", "AtmosphericProfilesLibrary", "CLIMAParameters", "CUDA", "ClimaComms", "ClimaCore", "ClimaTimeSteppers", "CloudMicrophysics", "Colors", "Dates", "Dierckx", "DiffEqBase", "DiffEqCallbacks", "Distributions", "DocStringExtensions", "FastGaussQuadrature", "ImageFiltering", "Insolation", "Interpolations", "IntervalSets", "JLD2", "LambertW", "LinearAlgebra", "Logging", "NCDatasets", "NVTX", "OrdinaryDiffEq", "Pkg", "Printf", "RRTMGP", "Random", "RootSolvers", "StaticArrays", "Statistics", "StatsBase", "SurfaceFluxes", "TerminalLoggers", "Test", "Thermodynamics", "YAML"]
-git-tree-sha1 = "ba828d47a976ed005ad0118758978d45bc7bb5a4"
+git-tree-sha1 = "ad4986fce23c7040b811a5da95ec424527524004"
 uuid = "b2c96348-7fb7-4fe0-8da9-78d88439e717"
-version = "0.15.4"
+version = "0.15.5"
 
 [[deps.ClimaComms]]
 deps = ["CUDA", "MPI"]
@@ -311,9 +311,9 @@ version = "0.3.0"
 
 [[deps.Compat]]
 deps = ["Dates", "LinearAlgebra", "UUIDs"]
-git-tree-sha1 = "5ce999a19f4ca23ea484e92a1774a61b8ca4cf8e"
+git-tree-sha1 = "e460f044ca8b99be31d35fe54fc33a5c33dd8ed7"
 uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
-version = "4.8.0"
+version = "4.9.0"
 
 [[deps.CompilerSupportLibraries_jll]]
 deps = ["Artifacts", "Libdl"]
@@ -408,15 +408,15 @@ version = "0.1.0+0"
 
 [[deps.DiffEqBase]]
 deps = ["ArrayInterface", "ChainRulesCore", "DataStructures", "Distributions", "DocStringExtensions", "EnumX", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "Printf", "RecursiveArrayTools", "Reexport", "Requires", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces", "ZygoteRules"]
-git-tree-sha1 = "c5692436e7f8279503466db216c74165d1b301e4"
+git-tree-sha1 = "ed586656058844e48660c6d6fdb384e83afc50db"
 uuid = "2b5f629d-d688-5b77-993f-72d75c75574e"
-version = "6.127.0"
+version = "6.128.0"
 
 [[deps.DiffEqCallbacks]]
 deps = ["DataStructures", "DiffEqBase", "ForwardDiff", "LinearAlgebra", "Markdown", "NLsolve", "Parameters", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"]
-git-tree-sha1 = "63b6be7b396ad395825f3cc48c56b53bfaf7e69d"
+git-tree-sha1 = "303ab70e4524843653e55e16a3dc7b75e677a3dd"
 uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def"
-version = "2.26.1"
+version = "2.27.0"
 
 [[deps.DiffResults]]
 deps = ["StaticArraysCore"]
@@ -796,15 +796,15 @@ version = "0.14.7"
 
 [[deps.IntervalSets]]
 deps = ["Dates", "Random", "Statistics"]
-git-tree-sha1 = "19ef25c6befb8076aefbc6f89d9011b415fb25da"
+git-tree-sha1 = "8e59ea773deee525c99a8018409f64f19fb719e6"
 uuid = "8197267c-284f-5f27-9208-e0e47529a953"
-version = "0.7.5"
+version = "0.7.7"
 
 [[deps.InverseFunctions]]
 deps = ["Test"]
-git-tree-sha1 = "eabe3125edba5c9c10b60a160b1779a000dc8b29"
+git-tree-sha1 = "68772f49f54b479fa88ace904f6127f0a3bb2e46"
 uuid = "3587e190-3f89-42d0-90ee-14403ec27112"
-version = "0.1.11"
+version = "0.1.12"
 
 [[deps.IrrationalConstants]]
 git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2"
@@ -1038,9 +1038,9 @@ version = "2.5.2"
 
 [[deps.LinearSolve]]
 deps = ["ArrayInterface", "DocStringExtensions", "EnumX", "FastLapackInterface", "GPUArraysCore", "InteractiveUtils", "KLU", "Krylov", "LinearAlgebra", "PrecompileTools", "Preferences", "RecursiveFactorization", "Reexport", "Requires", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Sparspak", "SuiteSparse", "UnPack"]
-git-tree-sha1 = "1b55771f2c211583ad52af5a5ca6475be374c961"
+git-tree-sha1 = "d2605a42d5453f510ca0fe37eff8aa0bfc5a3c80"
 uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
-version = "2.4.1"
+version = "2.4.2"
 
 [[deps.LogExpFunctions]]
 deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"]
@@ -1207,9 +1207,9 @@ version = "1.2.0"
 
 [[deps.NonlinearSolve]]
 deps = ["ArrayInterface", "DiffEqBase", "EnumX", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "PrecompileTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseDiffTools", "StaticArraysCore", "UnPack"]
-git-tree-sha1 = "2a7f28c62eb2c16b9c375c38f664cdcf22313cf5"
+git-tree-sha1 = "23dabe80f8ebec9a68b0db4cd02f2d2cdbc4f653"
 uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
-version = "1.8.0"
+version = "1.9.0"
 
 [[deps.OffsetArrays]]
 deps = ["Adapt"]
@@ -1276,9 +1276,9 @@ version = "1.6.2"
 
 [[deps.OrdinaryDiffEq]]
 deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "IfElse", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "LoopVectorization", "MacroTools", "MuladdMacro", "NLsolve", "NonlinearSolve", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLNLSolve", "SciMLOperators", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"]
-git-tree-sha1 = "4f1ab68f236fa846d0c30718c6b29c1665b019c0"
+git-tree-sha1 = "47c560dcb059570bdbd9f887a6b8958190e498a4"
 uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
-version = "6.53.3"
+version = "6.53.4"
 
 [[deps.PCRE2_jll]]
 deps = ["Artifacts", "Libdl"]
@@ -1311,9 +1311,9 @@ version = "0.12.3"
 
 [[deps.Parsers]]
 deps = ["Dates", "PrecompileTools", "UUIDs"]
-git-tree-sha1 = "4b2e829ee66d4218e0cef22c0a64ee37cf258c29"
+git-tree-sha1 = "716e24b21538abc91f6205fd1d8363f39b442851"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
-version = "2.7.1"
+version = "2.7.2"
 
 [[deps.Pipe]]
 git-tree-sha1 = "6842804e7867b115ca9de748a0cf6b364523c16d"
@@ -1545,9 +1545,9 @@ version = "0.1.8"
 
 [[deps.SciMLOperators]]
 deps = ["ArrayInterface", "DocStringExtensions", "Lazy", "LinearAlgebra", "Setfield", "SparseArrays", "StaticArraysCore", "Tricks"]
-git-tree-sha1 = "745755a5b932c9a664d7e9e4beb60c692b211d4b"
+git-tree-sha1 = "65c2e6ced6f62ea796af251eb292a0e131a3613b"
 uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961"
-version = "0.3.5"
+version = "0.3.6"
 
 [[deps.Scratch]]
 deps = ["Dates"]
@@ -1581,9 +1581,9 @@ version = "1.1.0"
 
 [[deps.SimpleNonlinearSolve]]
 deps = ["ArrayInterface", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "PackageExtensionCompat", "PrecompileTools", "Reexport", "SciMLBase", "StaticArraysCore"]
-git-tree-sha1 = "91fcc402c4ab978ad5759489db9a9c5a71732f2d"
+git-tree-sha1 = "20aa9831d654bab67ed561e78917047143ecb9bf"
 uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7"
-version = "0.1.18"
+version = "0.1.19"
 
 [[deps.SimpleTraits]]
 deps = ["InteractiveUtils", "MacroTools"]
@@ -1854,9 +1854,9 @@ version = "0.4.1"
 
 [[deps.Unitful]]
 deps = ["ConstructionBase", "Dates", "InverseFunctions", "LinearAlgebra", "Random"]
-git-tree-sha1 = "c4d2a349259c8eba66a00a540d550f122a3ab228"
+git-tree-sha1 = "1cd9b6d3f637988ca788007b7466c132feebe263"
 uuid = "1986cc42-f94f-5a68-af5c-568840ba703d"
-version = "1.15.0"
+version = "1.16.1"
 
 [[deps.UnitfulLatexify]]
 deps = ["LaTeXStrings", "Latexify", "Unitful"]

experiments/AMIP/modular/cli_options.jl

@@ -131,6 +131,10 @@ function argparse_settings()
         help = "Vertical diffusion [`false` (default), `VerticalDiffusion`, `true` (defaults to `VerticalDiffusion`)]"
         arg_type = String
         default = "false"
+        "--prognostic_surface"
+        help = "Determines if surface temperature is prognostic [`false` (default), , `true`, `PrognosticSurfaceTemperature`, `PrescribedSurfaceTemperature`]"
+        arg_type = String
+        default = "false"
         "--surface_setup"
         help = "Surface flux scheme [`DefaultExchangeCoefficients` (default), `DefaultMoninObukhov`]"
         arg_type = String